Figure S1

Annual number of sites surveyed, with a distinction between belonging exclusively to REFNET (green bars), exclusively to REPNET (brown bars) and to both networks.

Figure 1: Annual number of sites surveyed, with a distinction between belonging exclusively to REFNET (green bars), exclusively to REPNET (brown bars) and to both networks.

Figure S2

To assess the significance of a monotonous temporal trend for each sampling point, a Mann-Kendall non-parametric test is performed. Sen-Theil slope is then estimated in order to retrieve its sign. As the FBI score is a measure of degradation, both are positively correlated. Hence, if the trend is significant and the sign is positive, FBI scores tend to increase through time, reflecting a degradation of the river. On the contrary, a significant trend with a negative sign indicates an improvement of ‘river health’.

Figure 2: Map of the Fish-based index trends for the REPNET sites, with the hydrographic basins limits.

Figure S3

Description of taxa temporal trends using six indicators. Each point represents the annual median value of the indicator. Solid regression lines indicate that the Mann-Kendall trend test is statistically significant. The first two indicators “Density” and “Occupancy_rate” are fully described in the Methods section. The four other indicators are derived from the logistic models developed in Oberdorff et al. (2001) and giving the probability of occurrence of each of the 34 taxa as a function of a set of environmental characteristics. These models were originally fitted exclusively on reference (i.e. least-impacted) sites. We then considered a probability value over 50% as a predicted taxon presence and a probability below this threshold as a predicted taxon absence. These indicators are: (1) the percentage of sites where the taxon is predicted present and observed present (hereafter Confirmed_Presence), (2) the percentage of sites where the taxon taxon is predicted absent but observed present (hereafter Unexpected_Presence), (3) the percentage of sites where the taxon is predicted absent and observed absent (hereafter Confirmed_Absence) and (4) the percentage of sites where the taxon is predicted present but observed absent (hereafter Unexpected_Absence). When analyzed separately, these four indicators reflect temporal trends in the sites habitat suitability (or un-suitability) for a given taxon, according to the models.

Figure 3: Description of taxa temporal trends using six indicators. Each point represents the annual median value of the indicator. Solid regression lines indicate that the Mann-Kendall trend test is statistically significant. The first two indicators “Density” and “Occupancy_rate” are fully described in the Methods section. The four other indicators are derived from the logistic models developed in Oberdorff et al. (2001) and giving the probability of occurrence of each of the 34 taxa as a function of a set of environmental characteristics. These models were originally fitted exclusively on reference (i.e. least-impacted) sites. We then considered a probability value over 50% as a predicted taxon presence and a probability below this threshold as a predicted taxon absence. These indicators are: (1) the percentage of sites where the taxon is predicted present and observed present (hereafter Confirmed_Presence), (2) the percentage of sites where the taxon taxon is predicted absent but observed present (hereafter Unexpected_Presence), (3) the percentage of sites where the taxon is predicted absent and observed absent (hereafter Confirmed_Absence) and (4) the percentage of sites where the taxon is predicted present but observed absent (hereafter Unexpected_Absence). When analyzed separately, these four indicators reflect temporal trends in the sites habitat suitability (or un-suitability) for a given taxon, according to the models.

Table S1

Table 1: List of taxa contributing to each metric making up the FBI.
Taxon	total_nb_sp	nb_rheophilic_sp	nb_lithophilic_sp	total_dens_indiv	dens_tolerant_indiv	dens_invertivorous_indiv	dens_omnivorous_indiv
Alburnus alburnus	X			X	X		X
Anguilla anguilla	X			X		X
Barbus barbus	X	X	X	X
Barbus meridionalis	X	X	X	X
Telestes souffia	X	X		X
Rhodeus amarus	X			X
Abramis brama	X			X	X		X
Esox spp	X			X
Carassius spp	X			X			X
Cyprinus carpio	X			X			X
Cottus spp	X	X	X	X		X
Squalius cephalus	X			X	X		X
Gasterosteus aculeatus	X			X	X		X
Pungitius pungitius	X			X			X
Rutilus rutilus	X			X	X		X
Gobio spp	X			X		X
Gymnocephalus cernua	X			X		X
Chondrostoma nasus	X	X	X	X
Barbatula spp	X			X	X
Lota lota	X	X		X
Lampetra planeri	X		X	X
Thymallus spp	X	X	X	X		X
Ameiurus melas	X		X	X		X
Perca fluviatilis	X			X
Lepomis gibbosus	X			X		X
Scardinius erythrophthalmus	X			X			X
Sander lucioperca	X			X
Salmo salar	X	X	X	X		X
Alburnoides bipunctatus	X	X	X	X		X
Tinca tinca	X			X			X
Parachondrostoma toxostoma	X	X	X	X			X
Salmo trutta	X	X	X	X		X
Phoxinus spp	X		X	X
Leuciscus spp	X	X		X			X

Table S2

Table 2: Mann-Kendall test of monotonic temporal trend for the 25, 50 and 75 percentiles of annual FBI score for REPNET and REFNET, 2013-2013, excluding the sites that are shared between these networks. The rows in bold indicate a significant trend (mk_pvalue < 0.05).
network	period	variable	mk_pvalue	sens_slope	sig	trend
REFNET	2013-2023	p25	0.020	0.1233	TRUE	Degradation
REFNET	2013-2023	p50	0.062	0.0992	FALSE	No trend
REFNET	2013-2023	p75	0.008	0.1422	TRUE	Degradation
REPNET	2013-2023	p25	0.020	0.0635	TRUE	Degradation
REPNET	2013-2023	p50	0.436	0.0428	FALSE	No trend
REPNET	2013-2023	p75	0.043	0.1355	TRUE	Degradation

Table S3

Table 3: Count and proportion of the REPNET and REFNET sites according to the Fish-based index trends.
Degradation		Improvement		No trend
REPNET	REFNET	REPNET	REFNET	REPNET	REFNET
8.9% (n=124)	15.8% (n=49)	5.2% (n=73)	7.1% (n=22)	85.9% (n=1201)	77.1% (n=239)

The biological integrity of French rivers did not improve over the last seventeen years according to the national Fish-Based-Index (FBI)

Supplementary material

2024-03-28